1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951
|
# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
from functools import partial
from pathlib import Path
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pytest
from matplotlib.colors import PowerNorm, TwoSlopeNorm
from matplotlib.patches import Circle
from numpy.testing import assert_almost_equal, assert_array_equal, assert_equal
from mne import (
Epochs,
EvokedArray,
Projection,
compute_proj_evoked,
compute_proj_raw,
create_info,
find_layout,
make_fixed_length_events,
pick_types,
read_cov,
read_evokeds,
read_proj,
)
from mne._fiff.compensator import get_current_comp
from mne._fiff.constants import FIFF
from mne._fiff.pick import _picks_to_idx, channel_indices_by_type, pick_info
from mne._fiff.proj import make_eeg_average_ref_proj
from mne.channels import (
find_ch_adjacency,
make_dig_montage,
make_standard_montage,
read_layout,
)
from mne.datasets import testing
from mne.io import RawArray, read_info, read_raw_fif
from mne.preprocessing import (
ICA,
compute_bridged_electrodes,
compute_current_source_density,
)
from mne.time_frequency.tfr import AverageTFRArray
from mne.viz import plot_evoked_topomap, plot_projs_topomap, topomap
from mne.viz.tests.test_raw import _proj_status
from mne.viz.topomap import (
_get_pos_outlines,
_onselect,
plot_arrowmap,
plot_bridged_electrodes,
plot_ch_adjacency,
plot_psds_topomap,
plot_topomap,
)
from mne.viz.utils import _fake_click, _fake_keypress, _fake_scroll, _find_peaks
data_dir = testing.data_path(download=False)
subjects_dir = data_dir / "subjects"
ecg_fname = data_dir / "MEG" / "sample" / "sample_audvis_ecg-proj.fif"
triux_fname = data_dir / "SSS" / "TRIUX" / "triux_bmlhus_erm_raw.fif"
base_dir = Path(__file__).parents[2] / "io" / "tests" / "data"
evoked_fname = base_dir / "test-ave.fif"
raw_fname = base_dir / "test_raw.fif"
event_name = base_dir / "test-eve.fif"
ctf_fname = base_dir / "test_ctf_comp_raw.fif"
layout = read_layout("Vectorview-all")
cov_fname = base_dir / "test-cov.fif"
fast_test = dict(res=8, contours=0, sensors=False)
@pytest.mark.parametrize("layout", (None, "constrained"))
def test_plot_topomap_interactive(layout):
"""Test interactive topomap projection plotting."""
evoked = read_evokeds(evoked_fname, baseline=(None, 0))[0]
evoked.pick(picks="mag")
with evoked.info._unlock():
evoked.info["projs"] = []
assert not evoked.proj
evoked.add_proj(compute_proj_evoked(evoked, n_mag=1))
plt.close("all")
fig, ax = plt.subplots(layout=layout)
canvas = fig.canvas
kwargs = dict(
vlim=(-240, 240), times=[0.1], colorbar=False, axes=ax, res=8, time_unit="s"
)
evoked.copy().plot_topomap(proj=False, **kwargs)
canvas.draw()
image_noproj = np.array(canvas.buffer_rgba())
assert len(plt.get_fignums()) == 1
ax.clear()
evoked.copy().plot_topomap(proj=True, **kwargs)
canvas.draw()
image_proj = np.array(canvas.buffer_rgba())
assert not np.array_equal(image_noproj, image_proj)
assert len(plt.get_fignums()) == 1
ax.clear()
fig = evoked.copy().plot_topomap(proj="interactive", **kwargs)
canvas.draw()
image_interactive = np.array(canvas.buffer_rgba())
assert_array_equal(image_noproj, image_interactive)
assert not np.array_equal(image_proj, image_interactive)
assert len(plt.get_fignums()) == 2
proj_fig = plt.figure(plt.get_fignums()[-1])
assert _proj_status(fig, "matplotlib") == [False]
_fake_click(proj_fig, proj_fig.axes[0], [0.5, 0.5], xform="ax")
proj_fig.canvas.draw_idle()
assert _proj_status(fig, "matplotlib") == [True]
canvas.draw()
image_interactive_click = np.array(canvas.buffer_rgba())
corr = np.corrcoef(image_proj.ravel(), image_interactive_click.ravel())[0, 1]
assert 0.99 < corr <= 1
corr = np.corrcoef(image_noproj.ravel(), image_interactive_click.ravel())[0, 1]
assert 0.85 < corr < 0.9
_fake_click(proj_fig, proj_fig.axes[0], [0.5, 0.5], xform="ax")
canvas.draw()
image_interactive_click = np.array(canvas.buffer_rgba())
corr = np.corrcoef(image_noproj.ravel(), image_interactive_click.ravel())[0, 1]
assert 0.99 < corr <= 1
corr = np.corrcoef(image_proj.ravel(), image_interactive_click.ravel())[0, 1]
assert 0.85 < corr < 0.9
@testing.requires_testing_data
def test_plot_projs_topomap():
"""Test plot_projs_topomap."""
projs = read_proj(ecg_fname)
info = read_info(raw_fname)
plot_projs_topomap(projs, info=info, colorbar=True, **fast_test)
_, ax = plt.subplots()
projs[3].plot_topomap(info)
plot_projs_topomap(projs[:1], info, axes=ax, **fast_test) # test axes
triux_info = read_info(triux_fname)
plot_projs_topomap(triux_info["projs"][-1:], triux_info, **fast_test)
plot_projs_topomap(triux_info["projs"][:1], triux_info, **fast_test)
eeg_avg = make_eeg_average_ref_proj(info)
eeg_avg.plot_topomap(info, **fast_test)
# test vlims
for vlim in ("joint", (-1, 1), (None, 0.5), (0.5, None), (None, None)):
plot_projs_topomap(projs[:-1], info, vlim=vlim, colorbar=True)
eeg_proj = make_eeg_average_ref_proj(info)
info_meg = pick_info(info, pick_types(info, meg=True, eeg=False))
with pytest.raises(ValueError, match="Missing channels"):
plot_projs_topomap([eeg_proj], info_meg)
@pytest.mark.parametrize("vlim", ("joint", None))
@pytest.mark.parametrize("meg", ("combined", "separate"))
def test_plot_projs_topomap_joint(meg, vlim, raw):
"""Test that plot_projs_topomap works with joint vlim."""
if vlim is None:
vlim = (None, None)
projs = compute_proj_raw(raw, meg=meg)
fig = plot_projs_topomap(projs, info=raw.info, vlim=vlim, **fast_test)
assert len(fig.axes) == 4 # 2 mag, 2 grad
def test_plot_topomap_animation(capsys):
"""Test topomap plotting."""
# evoked
evoked = read_evokeds(evoked_fname, "Left Auditory", baseline=(None, 0))
# Test animation
_, anim = evoked.animate_topomap(
ch_type="grad", times=[0, 0.1], butterfly=False, time_unit="s", verbose="debug"
)
anim._func(1) # _animate has to be tested separately on 'Agg' backend.
out, _ = capsys.readouterr()
assert "extrapolation mode local to 0" in out
def test_plot_topomap_animation_csd(capsys):
"""Test topomap plotting of CSD data."""
# evoked
evoked = read_evokeds(evoked_fname, "Left Auditory", baseline=(None, 0))
evoked_csd = compute_current_source_density(evoked)
# Test animation
_, anim = evoked_csd.animate_topomap(
ch_type="csd", times=[0, 0.1], butterfly=False, time_unit="s", verbose="debug"
)
anim._func(1) # _animate has to be tested separately on 'Agg' backend.
out, _ = capsys.readouterr()
assert "extrapolation mode head to 0" in out
@pytest.mark.filterwarnings("ignore:.*No contour levels.*:UserWarning")
def test_plot_topomap_animation_nirs(fnirs_evoked, capsys):
"""Test topomap plotting for nirs data."""
fig, anim = fnirs_evoked.animate_topomap(ch_type="hbo", verbose="debug")
anim._func(1) # _animate has to be tested separately on 'Agg' backend.
out, _ = capsys.readouterr()
assert "extrapolation mode head to 0" in out
assert len(fig.axes) == 2
def test_plot_evoked_topomap_errors(evoked, monkeypatch):
"""Test error handling for evoked topomap plots."""
# simplify data and set some params to make the test really fast
evoked.pick(["EEG 001", "EEG 002"])
fast_func = partial(evoked.plot_topomap, res=8, contours=0, sensors=False)
fast_func_onetime = partial(fast_func, times=0.1)
# wrong channel type
with pytest.raises(ValueError, match="No channels of type 'mag'"):
fast_func(ch_type="mag")
# bad times
with pytest.raises(ValueError, match="Times should be between 0.0 and"):
fast_func(times=[-100])
with pytest.raises(ValueError, match="times must be 1D, got 2 dimensions"):
fast_func(times=[[0]])
# times / average mismatch
with pytest.raises(ValueError, match="3 time points.*2 periods for aver"):
fast_func([0.05, 0.1, 0.15], ch_type="eeg", average=[0.01, 0.02])
# average
with pytest.raises(ValueError, match="number of seconds.* got -1000.0"):
fast_func_onetime(average=-1e3)
with pytest.raises(TypeError, match="number of seconds.* got type:"):
fast_func_onetime(average="x")
# image_interp
with pytest.raises(RuntimeError, match="`image_interp` must be"):
fast_func_onetime(image_interp="bilinear")
# border
with pytest.raises(TypeError, match="be an instance of numeric or str"):
fast_func_onetime(extrapolate="head", border=[1, 2, 3])
with pytest.raises(ValueError, match="allowed value.*'mean'.*got 'fancy'"):
fast_func_onetime(extrapolate="head", border="fancy")
# projs
with pytest.raises(RuntimeError, match="Projs are already applied."):
fast_func_onetime(proj="interactive")
# too many subplots
with monkeypatch.context() as m: # speed it up by not actually plotting
m.setattr(topomap, "_plot_topomap", lambda *args, **kwargs: (None, None, None))
with pytest.warns(RuntimeWarning, match="More than 25 topomaps plots"):
fast_func([0.1] * 26, colorbar=False)
# missing channel locations
with evoked.info._unlock():
for ch in evoked.info["chs"]:
ch["loc"][:3] = 0.0
with pytest.raises(ValueError, match="points.*doesn't match.*channels."):
evoked.plot_topomap()
with evoked.info._unlock():
evoked.info["dig"] = None
with pytest.raises(RuntimeError, match="No digitization points found."):
evoked.plot_topomap()
@pytest.mark.parametrize(
"units, scalings, expected_unit",
[
(None, None, "µV"),
("foo", None, "foo"),
(None, 7.0, "AU"), # non-default scaling → "AU"
],
)
def test_plot_evoked_topomap_units(evoked, units, scalings, expected_unit):
"""Test that colorbar units respect scalings correctly."""
evoked.pick(["EEG 001", "EEG 002", "EEG 003"])
fig = evoked.plot_topomap(
times=0.1, res=8, contours=0, sensors=False, units=units, scalings=scalings
)
cbar = [ax for ax in fig.axes if hasattr(ax, "_colorbar")]
assert len(cbar) == 1
cbar = cbar[0]
assert cbar.get_title() == expected_unit
@pytest.mark.parametrize("extrapolate", ("box", "local", "head"))
def test_plot_evoked_topomap_extrapolation(evoked, extrapolate):
"""Test topomap extrapolation options."""
evoked.pick(["EEG 001", "EEG 002", "EEG 003"])
evoked.plot_topomap(
times=0.1, extrapolate=extrapolate, res=8, contours=0, sensors=False
)
def test_plot_evoked_topomap_border():
"""Test topomap extrapolation border values."""
# make some fake sensor locations: 25 sensors at distances of 0.2 to 1.0
# in steps of 0.2 in the ±x, ±y, and +z directions
ch_pos = np.array(
[
[
[r, 0, 0], # +x
[-r, 0, 0], # -x
[0, r, 0], # +y
[0, -r, 0], # -y
[0, 0, r], # +z
]
for r in np.linspace(0.2, 1, 5)
]
).reshape(-1, 3)
info = create_info(len(ch_pos), 250, "eeg")
ch_pos_dict = {name: pos for name, pos in zip(info["ch_names"], ch_pos)}
dig = make_dig_montage(ch_pos_dict, coord_frame="head")
info.set_montage(dig)
# simulate data
data = np.full(len(ch_pos), 5)
kwargs = dict(res=15, extrapolate="head", sphere=1, sensors=False)
idx = kwargs["res"] // 2
# when border=0...
img, _ = plot_topomap(data, info, border=0, **kwargs)
img_data = img.get_array().data
# middle pixel should exactly equal sensor data:
assert_equal(img_data[idx, idx], data[0])
# corner pixel should be close(ish) to zero:
assert img_data[0, 0] < 1.5
# when border='mean'...
img, _ = plot_topomap(data, info, border="mean", **kwargs)
img_data = img.get_array().data
# middle pixel should exactly equal sensor data:
assert_equal(img_data[idx, idx], data[0])
# and corner pixel should *also* be very close to sensor data:
assert_almost_equal(img_data[idx, idx], data[0], decimal=9)
@pytest.mark.slowtest
def test_plot_topomap_basic():
"""Test basics of topomap plotting."""
evoked = read_evokeds(evoked_fname, "Left Auditory", baseline=(None, 0))
res = 8
fast_test_noscale = dict(res=res, contours=0, sensors=False)
ev_bad = evoked.copy().pick(picks="eeg")
ev_bad.pick(ev_bad.ch_names[:2])
plt_topomap = partial(ev_bad.plot_topomap, **fast_test)
plt_topomap(times=ev_bad.times[:2] - 1e-6) # auto, plots EEG
evoked.plot_topomap(
[0.1],
ch_type="eeg",
scalings=1,
res=res,
contours=[-100, 0, 100],
time_unit="ms",
)
# test channel placement when only 'grad' are picked:
# ---------------------------------------------------
info_grad = evoked.copy().pick("grad").info
n_grads = len(info_grad["ch_names"])
data = np.random.randn(n_grads)
img, _ = plot_topomap(data, info_grad)
# check that channels are scattered around x == 0
pos = img.axes.collections[-1].get_offsets()
prop_channels_on_the_right = (pos[:, 0] > 0).mean()
assert prop_channels_on_the_right < 0.6
# other:
# ------
plt_topomap = partial(evoked.plot_topomap, **fast_test)
plt.close("all")
axes = [plt.subplot(221), plt.subplot(222)]
plt_topomap(axes=axes, colorbar=False)
plt.close("all")
plt_topomap(times=[-0.1, 0.2])
plt.close("all")
evoked_grad = evoked.copy().crop(0, 0).pick(picks="grad")
mask = np.zeros((204, 1), bool)
mask[[0, 3, 5, 6]] = True
names = []
def proc_names(x):
names.append(x)
return x[4:]
evoked_grad.plot_topomap(
ch_type="grad", times=[0], mask=mask, show_names=proc_names, **fast_test
)
want_names = np.array(evoked_grad.ch_names)[mask.squeeze()].tolist()
assert_equal(
[f"{name[:-1]}x" for name in want_names],
["MEG 011x", "MEG 012x", "MEG 013x", "MEG 014x"],
)
mask = np.zeros_like(evoked.data, dtype=bool)
mask[[1, 5], :] = True
plt_topomap(ch_type="mag", outlines=None)
times = [0.1]
plt_topomap(times, ch_type="grad", mask=mask)
plt_topomap(times, ch_type="planar1")
plt_topomap(times, ch_type="planar2")
plt_topomap(
times, ch_type="grad", mask=mask, show_names=True, mask_params={"marker": "x"}
)
plt.close("all")
p = plt_topomap(
times,
ch_type="grad",
image_interp="cubic",
show_names=lambda x: x.replace("MEG", ""),
)
subplot = [
x
for x in p.get_children()
if any(t in str(type(x)) for t in ("Axes", "Subplot"))
]
assert len(subplot) >= 1, [type(x) for x in p.get_children()]
subplot = subplot[0]
have_all = all(
"MEG" not in x.get_text()
for x in subplot.get_children()
if isinstance(x, matplotlib.text.Text)
)
assert have_all
# Plot array
for ch_type in ("mag", "grad"):
evoked_ = evoked.copy().pick(picks=ch_type)
plot_topomap(evoked_.data[:, 0], evoked_.info, **fast_test_noscale)
# fail with multiple channel types
pytest.raises(ValueError, plot_topomap, evoked.data[0, :], evoked.info)
# Test title
def get_texts(p):
return [
x.get_text()
for x in p.get_children()
if isinstance(x, matplotlib.text.Text)
]
p = plt_topomap(times, ch_type="eeg", average=0.01)
assert_equal(len(get_texts(p)), 0)
plt.close("all")
# Test averaging with a scalar input
averaging_times = [ev_bad.times[0], times[0], ev_bad.times[-1]]
p = plt_topomap(averaging_times, ch_type="eeg", average=0.01)
expected_ax_titles = (
"-0.200 – -0.195 s", # clipped on the left
"0.095 – 0.105 s", # full range
"0.494 – 0.499 s", # clipped on the right
)
for idx, expected_title in enumerate(expected_ax_titles):
assert p.axes[idx].get_title() == expected_title
# Test averaging with an array-like input
averaging_durations = [0.01, 0.02, None]
p = plt_topomap(averaging_times, ch_type="eeg", average=averaging_durations)
expected_ax_titles = (
"-0.200 – -0.195 s", # clipped on the left
"0.090 – 0.110 s", # full range
"0.499 s", # No averaging
)
for idx, expected_title in enumerate(expected_ax_titles):
assert p.axes[idx].get_title() == expected_title
del averaging_times, expected_ax_titles, expected_title
# delaunay triangulation warning
plt_topomap(times, ch_type="mag")
# change to no-proj mode
evoked = read_evokeds(evoked_fname, "Left Auditory", baseline=(None, 0), proj=False)
plt.close("all")
fig1 = evoked.plot_topomap(
"interactive", ch_type="mag", proj="interactive", **fast_test
)
# TODO: Clicking the slider creates a *new* image rather than updating
# the data directly. This makes it so that the projection is not applied
# to the correct matplotlib Image object.
# _fake_click(fig1, fig1.axes[1], (0.5, 0.5)) # click slider
data_max = np.max(fig1.axes[0].images[0]._A)
proj_fig = plt.figure(plt.get_fignums()[-1])
assert fig1.mne.proj_checkboxes.get_status() == [False, False, False]
pos = proj_fig.axes[0].texts[0].get_position() + np.array([0.01, 0])
_fake_click(proj_fig, proj_fig.axes[0], pos) # toggle projector
# make sure projector gets toggled
assert fig1.mne.proj_checkboxes.get_status() == [True, False, False]
assert np.max(fig1.axes[0].images[0]._A) != data_max
for ch in evoked.info["chs"]:
if ch["coil_type"] == FIFF.FIFFV_COIL_EEG:
ch["loc"].fill(0)
# Remove extra digitization point, so EEG digitization points
# correspond with the EEG electrodes
del evoked.info["dig"][85]
# Pass custom outlines without patch
eeg_picks = pick_types(evoked.info, meg=False, eeg=True)
pos, outlines = _get_pos_outlines(evoked.info, eeg_picks, 0.1)
evoked.plot_topomap(times, ch_type="eeg", outlines=outlines, **fast_test)
plt.close("all")
# Test interactive cmap
fig = plot_evoked_topomap(
evoked, times=[0.0, 0.1], ch_type="eeg", cmap=("Reds", True), **fast_test
)
_fake_keypress(fig, "up")
_fake_keypress(fig, " ")
_fake_keypress(fig, "down")
cbar = fig.get_axes()[0].CB # Fake dragging with mouse.
ax = cbar.cbar.ax
_fake_click(fig, ax, (0.1, 0.1))
_fake_click(fig, ax, (0.1, 0.2), kind="motion")
_fake_click(fig, ax, (0.1, 0.3), kind="release")
_fake_click(fig, ax, (0.1, 0.1), button=3)
_fake_click(fig, ax, (0.1, 0.2), button=3, kind="motion")
_fake_click(fig, ax, (0.1, 0.3), kind="release")
_fake_scroll(fig, 0.5, 0.5, -0.5) # scroll down
_fake_scroll(fig, 0.5, 0.5, 0.5) # scroll up
plt.close("all")
# Pass custom outlines with patch callable
def patch():
return Circle(
(0.5, 0.4687), radius=0.46, clip_on=True, transform=plt.gca().transAxes
)
outlines["patch"] = patch
plot_evoked_topomap(evoked, times, ch_type="eeg", outlines=outlines, **fast_test)
# Test error messages for invalid pos parameter
n_channels = len(pos)
data = np.ones(n_channels)
pos_1d = np.zeros(n_channels)
pos_3d = np.zeros((n_channels, 2, 2))
pytest.raises(ValueError, plot_topomap, data, pos_1d)
pytest.raises(ValueError, plot_topomap, data, pos_3d)
pytest.raises(ValueError, plot_topomap, data, pos[:3, :])
pos_x = pos[:, :1]
pos_xyz = np.c_[pos, np.zeros(n_channels)[:, np.newaxis]]
pytest.raises(ValueError, plot_topomap, data, pos_x)
pytest.raises(ValueError, plot_topomap, data, pos_xyz)
# An #channels x 4 matrix should work though. In this case (x, y, width,
# height) is assumed.
pos_xywh = np.c_[pos, np.zeros((n_channels, 2))]
plot_topomap(data, pos_xywh)
plt.close("all")
# Test peak finder
axes = [plt.subplot(131), plt.subplot(132)]
evoked.plot_topomap(times="peaks", axes=axes, **fast_test)
plt.close("all")
evoked.data = np.zeros(evoked.data.shape)
evoked.data[50][1] = 1
assert_array_equal(_find_peaks(evoked, 10), evoked.times[1])
evoked.data[80][100] = 1
assert_array_equal(_find_peaks(evoked, 10), evoked.times[[1, 100]])
evoked.data[2][95] = 2
assert_array_equal(_find_peaks(evoked, 10), evoked.times[[1, 95]])
assert_array_equal(_find_peaks(evoked, 1), evoked.times[95])
# Test excluding bads channels
evoked_grad.info["bads"] += [evoked_grad.info["ch_names"][0]]
orig_bads = evoked_grad.info["bads"]
evoked_grad.plot_topomap(ch_type="grad", times=[0], time_unit="ms")
assert_array_equal(evoked_grad.info["bads"], orig_bads)
def test_plot_psds_topomap_colorbar():
"""Test plot_psds_topomap colorbar option."""
raw = read_raw_fif(raw_fname)
picks = pick_types(raw.info, meg="grad")
info = pick_info(raw.info, picks)
freqs = np.arange(3.0, 9.5)
rng = np.random.default_rng(42)
psd = np.abs(rng.standard_normal((len(picks), len(freqs))))
bands = {"theta": [4, 8]}
plt.close("all")
fig_cbar = plot_psds_topomap(psd, freqs, info, colorbar=True, bands=bands)
assert len(fig_cbar.axes) == 2
fig_nocbar = plot_psds_topomap(psd, freqs, info, colorbar=False, bands=bands)
assert len(fig_nocbar.axes) == 1
def test_plot_tfr_topomap():
"""Test plotting of TFR data."""
raw = read_raw_fif(raw_fname)
times = np.linspace(-0.1, 0.1, 200)
res = 8
n_freqs = 3
nave = 1
rng = np.random.RandomState(42)
picks = [93, 94, 96, 97, 21, 22, 24, 25, 129, 130, 315, 316, 2, 5, 8, 11]
info = pick_info(raw.info, picks)
data = rng.randn(len(picks), n_freqs, len(times))
# test complex numbers
tfr = AverageTFRArray(
info=info,
data=data * (1 + 1j),
times=times,
freqs=np.arange(n_freqs),
nave=nave,
)
tfr.plot_topomap(
ch_type="mag", tmin=0.05, tmax=0.150, fmin=0, fmax=10, res=res, contours=0
)
# test real numbers
tfr = AverageTFRArray(
info=info, data=data, times=times, freqs=np.arange(n_freqs), nave=nave
)
tfr.plot_topomap(
ch_type="mag", tmin=0.05, tmax=0.150, fmin=0, fmax=10, res=res, contours=0
)
eclick = matplotlib.backend_bases.MouseEvent(
"button_press_event", plt.gcf().canvas, 0, 0, 1
)
eclick.xdata = eclick.ydata = 0.1
eclick.inaxes = plt.gca()
erelease = matplotlib.backend_bases.MouseEvent(
"button_release_event", plt.gcf().canvas, 0.9, 0.9, 1
)
erelease.xdata = 0.3
erelease.ydata = 0.2
pos = np.array([[0.11, 0.11], [0.25, 0.5], [0.0, 0.2], [0.2, 0.39]])
_onselect(eclick, erelease, tfr, pos, "grad", 1, 3, 1, 3, "RdBu_r", list())
_onselect(eclick, erelease, tfr, pos, "mag", 1, 3, 1, 3, "RdBu_r", list())
eclick.xdata = eclick.ydata = 0.0
erelease.xdata = erelease.ydata = 0.9
tfr._onselect(eclick, erelease, None, "mean", None)
plt.close("all")
# test plot_psds_topomap
info = raw.info.copy()
chan_inds = channel_indices_by_type(info)
info = pick_info(info, chan_inds["grad"][:4])
fig, axes = plt.subplots()
freqs = np.arange(3.0, 9.5)
bands = [(4, 8, "Theta")]
psd = np.random.rand(len(info["ch_names"]), freqs.shape[0])
plot_psds_topomap(psd, freqs, info, bands=bands, axes=[axes])
def test_ctf_plotting():
"""Test CTF topomap plotting."""
raw = read_raw_fif(ctf_fname, preload=True)
assert raw.compensation_grade == 3
events = make_fixed_length_events(raw, duration=0.01)
assert len(events) > 10
evoked = Epochs(raw, events, tmin=0, tmax=0.01, baseline=None).average()
assert get_current_comp(evoked.info) == 3
# smoke test that compensation does not matter
evoked.plot_topomap(time_unit="s")
# better test that topomaps can still be used without plotting ref
evoked.pick(picks="meg")
evoked.plot_topomap()
@pytest.mark.slowtest # can be slow on OSX
@testing.requires_testing_data
def test_plot_arrowmap(evoked):
"""Test arrowmap plotting."""
with pytest.raises(ValueError, match="Multiple channel types"):
plot_arrowmap(evoked.data[:, 0], evoked.info)
evoked_eeg = evoked.copy().pick("eeg")
with pytest.raises(ValueError, match="Multiple channel types"):
plot_arrowmap(evoked_eeg.data[:, 0], evoked.info)
evoked_mag = evoked.copy().pick("mag")
evoked_grad = evoked.pick("grad", exclude="bads")
plot_arrowmap(evoked_mag.data[:, 0], info_from=evoked_mag.info)
plot_arrowmap(
evoked_grad.data[:, 0], info_from=evoked_grad.info, info_to=evoked_mag.info
)
@testing.requires_testing_data
def test_plot_topomap_neuromag122():
"""Test topomap plotting."""
evoked = read_evokeds(evoked_fname, "Left Auditory", baseline=(None, 0))
evoked.pick(picks="grad")
evoked.pick(evoked.ch_names[:122])
ch_names = [f"MEG {k:03}" for k in range(1, 123)]
for c in evoked.info["chs"]:
c["coil_type"] = FIFF.FIFFV_COIL_NM_122
evoked.rename_channels(
{c_old: c_new for (c_old, c_new) in zip(evoked.ch_names, ch_names)}
)
layout = find_layout(evoked.info)
assert layout.kind.startswith("Neuromag_122")
evoked.plot_topomap(times=[0.1], **fast_test)
proj = Projection(
active=False,
desc="test",
kind=1,
data=dict(
nrow=1,
ncol=122,
row_names=None,
col_names=evoked.ch_names,
data=np.ones(122),
),
explained_var=0.5,
)
plot_projs_topomap([proj], evoked.info, **fast_test)
def test_plot_topomap_bads():
"""Test plotting topomap with bad channels (gh-7213)."""
data = np.random.RandomState(0).randn(3, 1000)
raw = RawArray(data, create_info(3, 1000.0, "eeg"))
ch_pos_dict = {name: pos for name, pos in zip(raw.ch_names, np.eye(3))}
raw.info.set_montage(make_dig_montage(ch_pos_dict, coord_frame="head"))
for count in range(3):
raw.info["bads"] = raw.ch_names[:count]
raw.info._check_consistency()
plot_topomap(data[:, 0], raw.info)
def test_plot_topomap_channel_distance():
"""
Test topomap plotting with spread out channels (gh-9511, gh-9526).
Test topomap plotting when the distance between channels is greater than
the head radius.
"""
ch_names = ["TP9", "AF7", "AF8", "TP10"]
info = create_info(ch_names, 100, ch_types="eeg")
evoked = EvokedArray(np.random.randn(4, 10) * 1e-6, info)
ten_five = make_standard_montage("standard_1005")
evoked.set_montage(ten_five)
evoked.plot_topomap(sphere=0.05, res=8)
def test_plot_topomap_bads_grad():
"""Test plotting topomap with bad gradiometer channels (gh-8802)."""
data = np.random.RandomState(0).randn(203)
info = read_info(evoked_fname)
info["bads"] = ["MEG 2242"]
picks = pick_types(info, meg="grad")
info = pick_info(info, picks)
assert len(info["chs"]) == 203
plot_topomap(data, info, res=8)
def test_plot_topomap_nirs_overlap(fnirs_epochs):
"""Test plotting nirs topomap with overlapping channels (gh-7414)."""
fig = fnirs_epochs["A"].average(picks="hbo").plot_topomap()
assert len(fig.axes) == 5
def test_plot_topomap_nirs_ica(fnirs_epochs):
"""Test plotting nirs ica topomap."""
pytest.importorskip("sklearn")
fnirs_epochs = fnirs_epochs.load_data().pick(picks="hbo")
fnirs_epochs = fnirs_epochs.pick(picks=range(30))
# fake high-pass filtering and hide the fact that the epochs were
# baseline corrected
with fnirs_epochs.info._unlock():
fnirs_epochs.info["highpass"] = 1.0
fnirs_epochs.baseline = None
ica = ICA().fit(fnirs_epochs)
fig = ica.plot_components()
assert len(fig[0].axes) == 20
def test_plot_cov_topomap():
"""Test plotting a covariance topomap."""
cov = read_cov(cov_fname)
info = read_info(evoked_fname)
cov.plot_topomap(info)
cov.plot_topomap(info, noise_cov=cov)
def test_plot_topomap_cnorm():
"""Test colormap normalization."""
rng = np.random.default_rng(42)
v = rng.uniform(low=-1, high=2.5, size=64)
v[:3] = [-1, 0, 2.5]
montage = make_standard_montage("biosemi64")
info = create_info(montage.ch_names, 256, "eeg").set_montage("biosemi64")
cnorm = TwoSlopeNorm(vmin=-1, vcenter=0, vmax=2.5)
# pass only cnorm, no vmin/vmax
plot_topomap(v, info, cnorm=cnorm)
# pass cnorm and vmin
with pytest.warns(RuntimeWarning, match="implicitly defines vmin=-1"):
plot_topomap(v, info, vlim=(-10, None), cnorm=cnorm)
# pass cnorm and vmax
with pytest.warns(RuntimeWarning, match="implicitly defines .* vmax=2.5"):
plot_topomap(v, info, vlim=(None, 10), cnorm=cnorm)
# try another subclass of mpl.colors.Normalize
plot_topomap(v, info, cnorm=PowerNorm(0.5))
def test_plot_bridged_electrodes():
"""Test plotting of bridged electrodes."""
rng = np.random.default_rng(42)
montage = make_standard_montage("biosemi64")
info = create_info(montage.ch_names, 256, "eeg").set_montage("biosemi64")
bridged_idx = [(0, 1), (2, 3)]
n_epochs = 10
ed_matrix = np.zeros((n_epochs, len(info.ch_names), len(info.ch_names))) * np.nan
triu_idx = np.triu_indices(len(info.ch_names), 1)
for i in range(n_epochs):
ed_matrix[i][triu_idx] = rng.random() + rng.random(triu_idx[0].size)
fig = plot_bridged_electrodes(
info,
bridged_idx,
ed_matrix,
topomap_args=dict(names=info.ch_names, vlim=(None, 1)),
)
# two bridged lines plus head outlines
assert len(fig.axes[0].lines) == 6
# test with sphere="eeglab"
fig = plot_bridged_electrodes(
info,
bridged_idx,
ed_matrix,
topomap_args=dict(names=info.ch_names, sphere="eeglab", vlim=(None, 1)),
)
with pytest.raises(RuntimeError, match="Expected"):
plot_bridged_electrodes(info, bridged_idx, np.zeros((5, 6, 7)))
# test with multiple channel types
raw = read_raw_fif(raw_fname, preload=True)
picks = _picks_to_idx(raw.info, "eeg")
raw._data[picks[0]] = raw._data[picks[1]] # artificially bridge electrodes
bridged_idx, ed_matrix = compute_bridged_electrodes(raw)
plot_bridged_electrodes(raw.info, bridged_idx, ed_matrix)
def test_plot_ch_adjacency():
"""Test plotting of adjacency matrix."""
xyz_pos = np.array(
[
[-0.1, 0.1, 0.1],
[0.1, 0.1, 0.1],
[0.0, 0.0, 0.12],
[-0.1, -0.1, 0.1],
[0.1, -0.1, 0.1],
]
)
info = create_info(list("abcde"), 23, ch_types="eeg")
montage = make_dig_montage(
ch_pos={ch: pos for ch, pos in zip(info.ch_names, xyz_pos)}, coord_frame="head"
)
info.set_montage(montage)
# construct adjacency
adj_sparse, ch_names = find_ch_adjacency(info, "eeg")
# plot adjacency
fig = plot_ch_adjacency(info, adj_sparse, ch_names, kind="2d", edit=True)
# find channel positions
collection = fig.axes[0].collections[0]
pos = collection.get_offsets().data
# get adjacency lines
lines = fig.axes[0].lines[4:] # (first four lines are head outlines)
# make sure lines match adjacency relations in the matrix
for line in lines:
x, y = line.get_data()
ch_idx = [
np.where((pos == [[x[ix], y[ix]]]).all(axis=1))[0][0] for ix in range(2)
]
assert adj_sparse[ch_idx[0], ch_idx[1]]
# make sure additional point is generated after clicking a channel
_fake_click(fig, fig.axes[0], pos[0], xform="data")
collections = fig.axes[0].collections
assert len(collections) == 2
# make sure the point is green
green = matplotlib.colors.to_rgba("tab:green")
assert (collections[1].get_facecolor() == green).all()
# make sure adjacency entry is modified after second click on another node
assert adj_sparse[0, 1]
assert adj_sparse[1, 0]
n_lines_before = len(lines)
_fake_click(fig, fig.axes[0], pos[1], xform="data")
assert not adj_sparse[0, 1]
assert not adj_sparse[1, 0]
# and there is one line less
lines = fig.axes[0].lines[4:]
n_lines_after = len(lines)
assert n_lines_after == n_lines_before - 1
# make sure there is still one green point ...
collections = fig.axes[0].collections
assert len(collections) == 2
assert (collections[1].get_facecolor() == green).all()
# ... but its at a different location
point_pos = collections[1].get_offsets().data
assert (point_pos == pos[1]).all()
# check that clicking again removes the green selection point
_fake_click(fig, fig.axes[0], pos[1], xform="data")
collections = fig.axes[0].collections
assert len(collections) == 1
# clicking the points again adds a green line
_fake_click(fig, fig.axes[0], pos[1], xform="data")
_fake_click(fig, fig.axes[0], pos[0], xform="data")
lines = fig.axes[0].lines[4:]
assert len(lines) == n_lines_after + 1
assert lines[-1].get_color() == "tab:green"
# smoke test for 3d option
adj = adj_sparse.toarray()
fig = plot_ch_adjacency(info, adj, ch_names, kind="3d")
# test errors
# -----------
# number of channels in the adjacency matrix and info must match
msg = (
"``adjacency`` must have the same number of rows as the number of "
"channels in ``info``"
)
with pytest.raises(ValueError, match=msg):
plot_ch_adjacency(info, adj_sparse, ch_names[:3], kind="2d")
# edition mode only available for 2d plot
msg = "Editing a 3d adjacency plot is not supported."
with pytest.raises(ValueError, match=msg):
plot_ch_adjacency(info, adj, ch_names, kind="3d", edit=True)
|